Tools

Available tools and plugins:

Where relevant please cite originating papers (#)
For bugs/issues and queries please contact the lab here


Galene.png

Platform: Standalone Windows and MacOS application
http://galene.flimfit.org/

As published in:
#Warren SC et al. eLife (2018) PubMed

Automated ECM fibre orientation and alignment script

Platform: FIJI / ImageJ
Download v1.08

As published in:
– Cazet A et al. Nature Communications (2018)
– Conway JRW et al. Scientific Reports (2017) PubMed
– Chou A et al. Gut (2017) PubMed
– Vennin C et al. Science Translational Medicine (2017) PubMed
#Mayorca-Guiliani AE*, Madsen CD*, Cox TR* et al. Nature Medicine (2017) PubMed

Automated Picrosirius Red (PR) analysis of collagen I using transmitted light

Platform: FIJI / ImageJ
Download v1.11

Automated Picrosirius Red (PR) birefringence (BRF) analysis of collagen I using polarised light

Platform: FIJI / ImageJ
Download v2.10

As published in:
– Conway JRW et al. Scientific Reports (2017) PubMed
– Chou A et al. Gut (2017) PubMed
#Vennin C et al. Science Translational Medicine (2017) PubMed

Automated Masson’s Trichrome Analysis of collagen I/bone (blue)

Platform: FIJI / ImageJ
Download v1.03